Adabifiroozjaei, E, Rastkerdar, E, Nemoto, Y, Nakayama, Y, Nishimiya, Y, Fronzi, M, Yao, Y, Nguyen, MT, Molina-Luna, L & Suzuki, TS 2023, 'In-situ scanning transmission electron microscopy study of Al-amorphous SiO2 layer-SiC interface', Journal of Materials Science, vol. 58, no. 6, pp. 2456-2468.
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AbstractHere, we present a comprehensive study on atomic-scale in-situ biasing/heating scanning transmission electron microscopy ((S)TEM) of Al-amorphous SiO2–SiC interface. The investigation includes electrical, chemical, and structural analysis of the interface at different temperatures (25–600 °C). The results show that at ~ 500 °C the electrical (three-orders of magnitude resistivity drop), chemical (dissolution of SiO2 amorphous layer), and microstructural features (e.g. formation of Al2O3, Si and Al4C3) of the interface start to change. According to the results, amorphous SiO2 dissolves in Al, leading to formation of α-Al2O3 and Si within the Al. In contrast, elemental interdiffusion (Al3+ ⇄ Si4+) between Al and SiC occurs resulting in formation of Al4C3. From the results, we can infer that reaction mechanism between Al and crystalline SiC is different with that between Al and SiO2 amorphous phase. It is believed that structural similarities between SiC and Al4C3 play an important role in paving the way for elemental interdiffusion.
Aisbett, J, Drinkwater, EJ, Quarrie, KL & Woodcock, S 2023, 'Applying generalized funnel plots to help design statistical analyses', Statistical Papers, vol. 64, no. 1, pp. 355-364.
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AbstractResearchers across many fields routinely analyze trial data using Null Hypothesis Significance Tests with zero null and p < 0.05. To promote thoughtful statistical testing, we propose a visualization tool that highlights practically meaningful effects when calculating sample sizes. The tool re-purposes and adapts funnel plots, originally developed for meta-analyses, after generalizing them to cater for meaningful effects. As with traditional sample size calculators, researchers must nominate anticipated effect sizes and variability alongside the desired power. The advantage of our tool is that it simultaneously presents sample sizes needed to adequately power tests for equivalence, for non-inferiority and for superiority, each considered at up to three alpha levels and in positive and negative directions. The tool thus encourages researchers at the design stage to think about the type and level of test in terms of their research goals, costs of errors, meaningful effect sizes and feasible sample sizes. An R-implementation of the tool is available on-line.
Ashique, S, Gupta, K, Gupta, G, Mishra, N, Singh, SK, Wadhwa, S, Gulati, M, Dureja, H, Zacconi, F, Oliver, BG, Paudel, KR, Hansbro, PM, Chellappan, DK & Dua, K 2023, 'Vitamin D—A prominent immunomodulator to preventCOVID‐19 infection', International Journal of Rheumatic Diseases, vol. 26, no. 1, pp. 13-30.
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Bai, L, Song, A, Wang, L, Lei, X, Zhang, T, Tian, H, Liu, H, Qin, X, Wang, G & Shao, G 2023, 'Enhancement of hydrogen desorption for electrocatalytic hydrogen evolution on nickel-coupled graphite carbon nitride catalysts', Ionics, vol. 29, no. 1, pp. 323-330.
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Bates, H, Zavafer, A, Szabó, M & Ralph, PJ 2023, 'The slow-phase of chlorophyll fluorescence induction curve reflects the electron transport rates of Photosystem II in vivo in Chlorella vulgaris', Journal of Applied Phycology, vol. 35, no. 1, pp. 109-116.
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Becker, A, Lowry, MB, Fowler, AM & Taylor, MD 2023, 'Hydroacoustic surveys reveal the distribution of mid-water fish around two artificial reef designs in temperate Australia', Fisheries Research, vol. 257, pp. 106509-106509.
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Bhaskaran, A & Wand, MP 2023, 'Dispersion parameter extension of precise generalized linear mixed model asymptotics', Statistics & Probability Letters, vol. 193, pp. 109691-109691.
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Bordin, DM, Bishop, D, de Campos, EG, Blanes, L, Doble, P, Roux, C & De Martinis, BS 2023, 'Analysis of Stimulants in Sweat and Urine Using Disposable Pipette Extraction and Gas Chromatography Coupled to Mass Spectrometry in the Context of Doping Control', Journal of Analytical Toxicology, vol. 46, no. 9, pp. 991-998.
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Abstract
Urine is initially collected from athletes to screen for the presence of illicit drugs. Sweat is an alternative sample matrix that provides advantages over urine including reduced opportunity for sample adulteration, longer detection-time window and non-invasive collection. Sweat is suitable for analysis of the parent drug and metabolites. In this study, a method was developed and validated to determine the presence of 13 amphetamine- and cocaine-related substances and their metabolites in sweat and urine using disposable pipette extraction (DPX) by gas chromatography coupled to mass spectrometry. The DPX extraction was performed using 0.1 M HCl and dichloromethane:isopropanol:ammonium hydroxide (78:20:2, v/v/v) followed by derivatization with N-methyl-N-(trimethylsilyl) trifluoroacetamide at 90°C for 20 min. DPX extraction efficiencies ranged between 65.0% and 96.0% in urine and 68.0% and 101.0% in sweat. Method accuracy was from 90.0% to 104.0% in urine and from 89.0% to 105.0% in sweat. Intra-assay precision in urine and in sweat were <15.6% and <17.8%, respectively, and inter-assay precision ranged from 4.70% to 15.3% in urine and from 4.05% to 15.4% in sweat. Calibration curves presented a correlation coefficient –0.99 for all analytes in both matrices. The validated method was applied to urine and sweat samples collected from 40 professional athletes who knowingly took one or more of the target illicit drugs. Thirteen of 40 athletes were positive for at least one drug. All the drugs detected in the urine were also detected in sweat samples indicating that sweat is a viable matrix for screening or confirmatory drug testing.
Brown, AO, Ueland, M, Stuart, BH & Frankham, GJ 2023, 'A forensically validated genetic toolkit for the species and lineage identification of the highly trafficked shingleback lizard (Tiliqua rugosa)', Forensic Science International: Genetics, vol. 62, pp. 102784-102784.
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Carbonara, K, Padula, MP & Coorssen, JR 2023, 'Quantitative assessment confirms deep proteome analysis by integrative top–down proteomics', ELECTROPHORESIS, vol. 44, no. 3-4, pp. 472-480.
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Chen, H, Kimyon, O, Chen, R, Gunawan, C, Ramandi, HL, Canbulat, I & Saydam, S 2023, 'The effectiveness of epoxy coating for preventing microbially induced corrosion of rock bolts', IOP Conference Series: Earth and Environmental Science, vol. 1124, no. 1, pp. 012097-012097.
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Abstract
In the past two decades, the corrosion failures of rock reinforcement bolts in underground coal mines have been increasingly reported. Preliminary studies have shown that these failures were predominantly related to pitting and stress corrosion cracking. The analyses in affected mines indicated microbially induced corrosion (MIC) as one of the primary corrosion causes. As such, there is an urgent demand from industries to develop methods to mitigate MIC-associated failures of rock bolts in underground coal mines. This study examined epoxy coating to determine its effectiveness in preventing biofilm formation on steel surfaces and, in turn, averting MIC. The corrosion-causing bacteria were isolated and enriched from groundwater samples collected from the affected mine sites. Coated and uncoated rock bolt samples were prepared from the bolts and incubated in media in the absence and presence of the corrosion-causing bacteria. Fluorescence microscopy imaging found no evidence of bacterial biomass growth on the surface of the epoxy-coated steel surfaces after 30 days, while the non-coated surfaces were colonised by biomass. The observations suggest the potential of epoxy coating for bolt MIC prevention. Future studies to assess the applicability of epoxy coating in the underground mine environment are recommended.
Chen, Y, Li, C, Yang, T, Ekimov, EA, Bradac, C, Ha, ST, Toth, M, Aharonovich, I & Tran, TT 2023, 'Real-Time Ratiometric Optical Nanoscale Thermometry', ACS Nano, vol. 17, no. 3, pp. 2725-2736.
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Clain, C, Stewart, J, Fowler, A & Diamond, S 2023, 'Reproductive biology of largehead hairtail (Trichiurus lepturus) in south-eastern Australia', Aquaculture and Fisheries, vol. 8, no. 2, pp. 148-158.
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Knowledge of reproductive biology and life-history traits of populations exploited by fisheries is important for their sustainable management. We investigated the life-history traits of Trichiurus lepturus (largehead hairtail) in south-eastern Australia; a region of low exploitation for this otherwise heavily exploited circumglobal species, to investigate whether there were differences in the reproductive biology and life-history traits in the south-east Australian population compared with those in other regions. We also used histological sections to examine male and female gonads at a microscopic level. Trichiurus lepturus in south-eastern Australia had a greater maximum length (193 cm total length (TL)), matured at a larger length (108 cm TL at 50% mature) and had a spawning period (March to September, Austral winter) that was inconsistent with other regions. The overall sex ratio of 1:0.4 females: males was consistent with a female dominant sex ratio observed in other regions, particularly in larger length classes. However, females in the current study dominated samples from both estuarine and coastal habitats, as well as during the spawning and non-spawning periods, which is not consistent with the patterns found in other regions. Differences in south-eastern Australia may relate to limited fishing pressure, genetic variation, or differences in environmental factors that influence reproductive development, including temperature, trophic resources and habitat.
Collins, S, Stuart, B & Ueland, M 2023, 'The use of lipids from textiles as soft-tissue biomarkers of human decomposition', Forensic Science International, vol. 343, pp. 111547-111547.
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Cooper, GE, Mayall, J, Donovan, C, Haw, TJ, Budden, KF, Hansbro, NG, Blomme, EE, Maes, T, Kong, CW, Horvat, JC, Khakoo, SI, Wilkinson, TMA, Hansbro, PM & Staples, KJ 2023, 'Antiviral Responses of Tissue-resident CD49a+ Lung Natural Killer Cells Are Dysregulated in Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 207, no. 5, pp. 553-565.
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Dhungana, A, Becchi, S, Leake, J, Morris, G, Avgan, N, Balleine, BW, Vissel, B & Bradfield, LA 2023, 'Goal-Directed Action Is Initially Impaired in a hAPP-J20 Mouse Model of Alzheimer’s Disease', eneuro, vol. 10, no. 2, pp. ENEURO.0363-22.2023.
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AbstractCognitive-behavioral testing in preclinical models of Alzheimer’s disease has failed to capture deficits in goal-directed action control. Here, we provide the first comprehensive investigation of goal-directed action in a transgenic mouse model of Alzheimer’s disease. Specifically, we tested outcome devaluation performance in male and female human amyloid precursor protein (hAPP)-J20 mice. Mice were first trained to press left and right levers for pellet and sucrose outcomes, respectively (counterbalanced), over 4 d. On test, mice were prefed one of the outcomes to satiety and given a choice between levers. Devaluation performance was intact for 36-week-old wild-types of both sexes, who responded more on the valued relative to the devalued lever (Valued > Devalued). By contrast, devaluation was impaired (Valued = Devalued) for J20 mice of both sexes, and for 52-week-old male mice regardless of genotype. After additional lever press training (i.e., 8-d lever pressing in total), devaluation was intact for all mice, demonstrating that the initial deficits were not a result of a nonspecific impairment in reward processing, depression, or locomotor activity in J20 or aging mice. Follow-up analyses revealed that microglial expression in the dorsal CA1 region of the hippocampus was associated with poorer outcome devaluation performance on initial, but not later tests. Together, these data demonstrate that goal-directed action is initially impaired in J20 mice of both sexes and in aging male mice regardless of genotype, and that this impairment is related to neuroinflammation in the dorsal CA1 hippocampal region.
Dilernia, NJ, Camp, EF, Bartels, N & Suggett, DJ 2023, 'Contrasting the thermal performance of cultured coral endosymbiont photo-physiology', Journal of Experimental Marine Biology and Ecology, vol. 561, pp. 151865-151865.
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Ding, Y, Zhang, S, Li, J, Sun, Y, Yin, B, Li, H, Ma, Y, Wang, Z, Ge, H, Su, D & Ma, T 2023, 'Enhanced Elastic Migration of Magnesium Cations in alpha‐Manganese Dioxide Tunnels Locally Tuned by Aluminium Substitution', Advanced Functional Materials, vol. 33, no. 2, pp. 2210519-2210519.
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The harsh conditions of large hydrated ion radius of Mg2+ cations and the strong electrostatic interaction with the host material put forward higher requirements for high-performance aqueous magnesium ion (Mg2+) energy storage devices. Herein, substituted aluminium ions (Al3+) doped α-MnO2 materials are prepared. The introduction of Al3+ cations adjust the local chemical environment inside the tunnel structure of α-MnO2 and precisely regulates the diffusion behavior of inserted Mg2+ cations. The shortened oxygens’ distance and abundant oxygen defects result in a substantially enhanced elastic migration pattern of Mg2+ cations driven by strengthened electrostatic attraction, which brings the lower diffusion energy barrier, improved reaction kinetics, and adaptive volume expansion as evidenced by Climbing Image-Nudged Elastic Band density function theory calculations coupled with experimental confirmation in X-ray photoelectron spectroscopy, electron paramagnetic resonance, and galvanostatic intermittent titration technique. As a result, this rationally designed cathode exhibits a high reversible capacity of 197.02 mAh g-1 at 0.1 A g-1 and stable cycle performance of 2500 cycles with 82% retention. These parameters are among the best of Mg-ion capacitors reported to date. This study offers a detailed insight into the local tunnel structure tunning effect and opens up a new path of modification for tunnel-type structural materials.
DOOLEY, AH & JIN, JIE 2023, 'A non-singular version of the Oseledeč ergodic theorem', Ergodic Theory and Dynamical Systems, vol. 43, no. 3, pp. 873-886.
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AbstractKingman’s subadditive ergodic theorem is traditionally proved in the setting of a measure-preserving invertible transformation T of a measure space
$(X, \mu )$
. We use a theorem of Silva and Thieullen to extend the theorem to the setting of a not necessarily invertible transformation, which is non-singular under the assumption that
$\mu $
and
$\mu \circ T$
have the same null sets. Using this, we are able to produce versions of the Furstenberg–Kesten theorem and the Oseledeč ergodic theorem for products of random matrices without the assumption that the transformation is either invertible or measure-preserving.
Dowling, NA, Wilson, JR, Cope, JM, Dougherty, DT, Lomonico, S, Revenga, C, Snouffer, BJ, Salinas, NG, Torres‐Cañete, F, Chick, RC, Fowler, AM & Parma, AM 2023, 'The FishPath approach for fisheries management in a data‐ and capacity‐limited world', Fish and Fisheries, vol. 24, no. 2, pp. 212-230.
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Drew-Smythe, JJ, Davila, YC, McLean, CM, Hingee, MC, Murray, ML, Webb, JK, Krix, DW & Murray, BR 2023, 'Community perceptions of ecosystem services and disservices linked to urban tree plantings', Urban Forestry & Urban Greening, vol. 82, pp. 127870-127870.
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Elankumuran, P, Browning, GF, Marenda, MS, Kidsley, A, Osman, M, Haenni, M, Johnson, JR, Trott, DJ, Reid, CJ & Djordjevic, SP 2023, 'Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans', Microbial Genomics, vol. 9, no. 2.
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ST372 are widely reported as the major
Escherichia coli
sequence type in dogs globally. They are also a sporadic cause of extraintestinal infections in humans. Despite this, it is unknown whether ST372 strains from dogs and humans represent shared or distinct populations. Furthermore, little is known about genomic traits that might explain the prominence of ST372 in dogs or presence in humans. To address this, we applied a variety of bioinformatics analyses to a global collection of 407 ST372
E. coli
whole-genome sequences to characterize their epidemiological features, population structure and associated accessory genomes. We confirm that dogs are the dominant host of ST372 and that clusters within the population structure exhibit distinctive O:H types. One phylogenetic cluster, ‘cluster M', comprised almost half of the sequences and showed the divergence of two human-restricted clades that carried different O:H types to the remainder of the cluster. We also present evidence supporting transmission between dogs and humans within different clusters of the phylogeny, including M. We show that multiple acquisitions of the pdu propanediol utilization operon have occurred in clusters dominated by isolates of canine source, possibly linked to diet, whereas loss of the
Faiz, A, Pavlidis, S, Kuo, C-H, Rowe, A, Hiemstra, PS, Timens, W, Berg, M, Wisman, M, Guo, Y-K, Djukanović, R, Sterk, P, Meyer, KB, Nawijn, MC, Adcock, I, Chung, KF & van den Berge, M 2023, 'Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD', Thorax, vol. 78, no. 4, pp. 335-343.
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RationaleSevere asthma and chronic obstructive pulmonary disease (COPD) share common pathophysiological traits such as relative corticosteroid insensitivity. We recently published three transcriptome-associated clusters (TACs) using hierarchical analysis of the sputum transcriptome in asthmatics from the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort comprising one Th2-high inflammatory signature (TAC1) and two Th2-low signatures (TAC2 and TAC3).ObjectiveWe examined whether gene expression signatures obtained in asthma can be used to identify the subgroup of patients with COPD with steroid sensitivity.MethodsUsing gene set variation analysis, we examined the distribution and enrichment scores (ES) of the 3 TACs in the transcriptome of bronchial biopsies from 46 patients who participated in the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease COPD study that received 30 months of treatment with inhaled corticosteroids (ICS) with and without an added long-acting β-agonist (LABA). The identified signatures were then associated with longitudinal clinical variables after treatment. Differential gene expression and cellular convolution were used to define key regulated genes and cell types.Measurements and main resultsBronchial biopsies in patients with COPD at baseline showed a wide range of expression of the 3 TAC signatures. After ICS±LABA treatment, the ES of TAC1 was significantly reduced at 30 months, but those of TAC2 and TAC3 were unaffected. A corticosteroid-sensitive TAC1 signature was developed from the TAC1 ICS-responsive genes. This signature consisted of mast cell-specific genes identified by single-cell RNA-sequencing and positively correlated with bronchial b...
Fang, H, Liu, Y, Chen, C-H & Hwang, F-J 2023, 'Travel Time Prediction Method Based on Spatial-Feature-based Hierarchical Clustering and Deep Multi-input Gated Recurrent Unit', ACM Transactions on Sensor Networks, vol. 19, no. 2, pp. 1-21.
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Accurate
travel time prediction (TTP)
is a significant aspect in the
intelligent transportation system (ITS)
. Travel times of certain road segments explicitly reflect the traffic conditions of those sections. Effective TTP of road segments is instrumental in route planning, traffic control, and traffic management. However, the accuracy of TTP is greatly affected by the intricate topological structure of traffic network and the dynamics of traffic flow over time. This paper develops a TTP method based on the
spatial-feature-based hierarchical clustering (SFHC)
and
deep multi-input gated recurrent unit (DMGRU)
. The proposed two-stage method is capable of capturing the spatial-temporal features of traffic network. Specifically, the SFHC divides the road segments into several clusters having similar traffic features, and then the clustered data is fed into the DMGRU for TTP. Our experiments conducted on the practical dataset demonstrate that the designed prediction method can achieve the
mean absolute percentage error (MAPE)
of 3.3109% and
mean absolute error (MAE)
of 2.5658, which outperform various combinations of baseline clustering algorithms and prediction models.
Firme, GF, Hughes, DJ, Laiolo, L, Roughan, M, Suthers, IM & Doblin, MA 2023, 'Contrasting phytoplankton composition and primary productivity in multiple mesoscale eddies along the East Australian coast', Deep Sea Research Part I: Oceanographic Research Papers, vol. 193, pp. 103952-103952.
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Fleming, CL, Golzan, M, Gunawan, C & McGrath, KC 2023, 'Systematic and Bibliometric Analysis of Magnetite Nanoparticles and Their Applications in (Biomedical) Research', Global Challenges, vol. 7, no. 1, pp. 2200009-2200009.
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Fu, S, Shi, W, Luo, T, He, Y, Zhou, L, Yang, J, Yang, Z, Liu, J, Liu, X, Guo, Z, Yang, C, Liu, C, Huang, Z-L, Ries, J, Zhang, M, Xi, P, Jin, D & Li, Y 2023, 'Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging', Nature Methods, vol. 20, no. 3, pp. 459-468.
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Gertner, DS, Violi, JP, Bishop, DP & Padula, MP 2023, 'Lipid Spectrum Generator: A Simple Script for the Generation of Accurate In Silico Lipid Fragmentation Spectra', Analytical Chemistry, vol. 95, no. 5, pp. 2909-2916.
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Ghorbanpour, SM, Richards, C, Pienaar, D, Sesperez, K, Aboulkheyr Es., H, Nikolic, VN, Karadzov Orlic, N, Mikovic, Z, Stefanovic, M, Cakic, Z, Alqudah, A, Cole, L, Gorrie, C, McGrath, K, Kavurma, MM, Ebrahimi Warkiani, M & McClements, L 2023, 'A placenta-on-a-chip model to determine the regulation of FKBPL and galectin-3 in preeclampsia', Cellular and Molecular Life Sciences, vol. 80, no. 2.
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AbstractPreeclampsia is a pregnancy-specific cardiovascular disorder, involving significant maternal endothelial dysfunction. Although inappropriate placentation due to aberrant angiogenesis, inflammation and shallow trophoblast invasion are the root causes of preeclampsia, pathogenic mechanisms are poorly understood, particularly in early pregnancy. Here, we first confirm the abnormal expression of important vascular and inflammatory proteins, FK506-binding protein-like (FKBPL) and galectin-3 (Gal-3), in human plasma and placental tissues from women with preeclampsia and normotensive controls. We then employ a three-dimensional microfluidic placental model incorporating human umbilical vein endothelial cells (HUVECs) and a first trimester trophoblast cell line (ACH-3P) to investigate FKBPL and Gal-3 signaling in inflammatory conditions. In human samples, both circulating (n = 17 controls; n = 30 preeclampsia) and placental (n ≥ 6) FKBPL and Gal-3 levels were increased in preeclampsia compared to controls (plasma: FKBPL, p < 0.0001; Gal-3, p < 0.01; placenta: FKBPL, p < 0.05; Gal-3, p < 0.01), indicative of vascular dysfunction in preeclampsia. In our placenta-on-a-chip model, we show that endothelial cells are critical for trophoblast-mediated migration and that trophoblasts effectively remodel endothelial vascular networks. Inflammatory cytokine tumour necrosis factor-α (10 ng/mL) modulates both FKBPL and Gal-3 signaling in conjunction with trophoblast migration and impairs vascular network formation (p < 0.005). Our placenta-on-a-chip recapitulates aspects of inappropriate placental development and vascular dysfunction in preeclampsia.
Gilchrist, AM, Wu, X, Hawkins, BA, Hibbs, DE & Gale, PA 2023, 'Fluorinated tetrapodal anion transporters', iScience, vol. 26, no. 2, pp. 105988-105988.
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Goh, YF, Røder, HL, Chan, SH, Ismail, MH, Madsen, JS, Lee, KWK, Sørensen, SJ, Givskov, M, Burmølle, M, Rice, SA & McDougald, D 2023, 'Associational Resistance to Predation by Protists in a Mixed Species Biofilm', Applied and Environmental Microbiology, vol. 89, no. 2.
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Biofilms have been shown to protect bacterial cells from predation by protists. Biofilm studies have traditionally used single species systems, which have provided information on the mechanisms and regulation of biofilm formation and dispersal, and the effects of predation on these biofilms.
Goodswen, SJ, Kennedy, PJ & Ellis, JT 2023, 'A guide to current methodology and usage of reverse vaccinology towards in silico vaccine discovery', FEMS Microbiology Reviews, vol. 47, no. 2.
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Abstract
Reverse vaccinology (RV) was described at its inception in 2000 as an in silico process that starts from the genomic sequence of the pathogen and ends with a list of potential protein and/or peptide candidates to be experimentally validated for vaccine development. Twenty-two years later, this process has evolved from a few steps entailing a handful of bioinformatics tools to a multitude of steps with a plethora of tools. Other in silico related processes with overlapping workflow steps have also emerged with terms such as subtractive proteomics, computational vaccinology, and immunoinformatics. From the perspective of a new RV practitioner, determining the appropriate workflow steps and bioinformatics tools can be a time consuming and overwhelming task, given the number of choices. This review presents the current understanding of RV and its usage in the research community as determined by a comprehensive survey of scientific papers published in the last seven years. We believe the current mainstream workflow steps and tools presented here will be a valuable guideline for all researchers wanting to apply an up-to-date in silico vaccine discovery process.
Gow, I, Smith, N, Stark, D & Ellis, J 2023, 'Molecular Detection of Neglected Tropical Diseases: The Case for Automated Near–Point-of-Care Diagnosis of Leishmaniasis', The American Journal of Tropical Medicine and Hygiene, vol. 108, no. 1, pp. 2-6.
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ABSTRACT.
Neglected tropical diseases affect those in poorer nations disproportionately across the globe. One example of these, leishmaniasis, is a debilitating and potentially fatal parasitic infection. Molecular detection of this disease can provide accurate and fast diagnosis, and with near point-of-care technologies, detection can be provided in many health-care settings. Traditionally, the perceived limitations to such detection methods have hindered their provision to resource-limited nations, but new technologies and techniques are helping to overcome these perceptions. The current pandemic offers an opportunity to maintain and develop further advances, ensuring molecular diagnostics are accessible to all.
Gu, H, Lam, HC, Pham, TTT & Zinder, Y 2023, 'Heuristics and meta-heuristic to solve the ROADEF/EURO challenge 2020 maintenance planning problem', Journal of Heuristics, vol. 29, no. 1, pp. 139-175.
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Guo, C, Chen, C-H, Chang, C-C, Hwang, F-J & Chang, C-C 2023, 'De-Correlation Neural Network for Synchronous Implementation of Estimation and Secrecy', IEEE Communications Letters, vol. 27, no. 1, pp. 165-169.
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Gupta, G, Alharbi, KS, Javed Shaikh, MA, Imam, SS, Alshehri, S, Ghoneim, MM, Almalki, WH, Singh, SK, Kumar, D, Kumar, AP, Dua, K, Chellappan, DK & Paudel, KR 2023, 'Role of Flavonoids in Management of Various Biological Targets inAlzheimer’s Disease: Evidence from Preclinical to Clinical Studies', Current Medicinal Chemistry, vol. 30, no. 18, pp. 2061-2074.
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Abstract:
More than 10 million people worldwide have Alzheimer's disease (AD), a degenerative neurological illness and the most prevalent form of dementia. AD's progression in memory loss, cognitive deterioration, and behavioral changes are all symptoms. Amyloid-beta 42 (Aβ42), the hyperphosphorylated forms of microtubule-associated tau protein, and other cellular and systemic alterations are all factors that contribute to cognitive decline in AD. Rather than delivering a possible cure, present therapy strategies focus on reducing disease symptoms. It has long been suggested that various naturally occurring small molecules (plant extract products and microbiological isolates, for example) could be beneficial in preventing or treating disease. Small compounds, such as flavonoids, have attracted much interest recently due to their potential to alleviate cellular stress. Flavonoids have been proven helpful in various ways, including antioxidants, anti-inflammatory agents, and anti-apoptotic agents, but their mechanism remains unknown. The flavonoid therapy of Alzheimer's disease focuses on this review, which includes a comprehensive literature analysis.
Haifer, C, Luu, LDW, Paramsothy, S, Borody, TJ, Leong, RW & Kaakoush, NO 2023, 'Microbial determinants of effective donors in faecal microbiota transplantation for UC', Gut, vol. 72, no. 1, pp. 90-100.
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ObjectiveFaecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection.DesignFaecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomicsResultsGut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics.ConclusionDonor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host.Trial regist...
Harris, RJ, Bryant, C, Coleman, MA, Leigh, A, Briceño, VF, Arnold, PA & Nicotra, AB 2023, 'A novel and high‐throughput approach to assess photosynthetic thermal tolerance of kelp using chlorophyll α fluorometry', Journal of Phycology, vol. 59, no. 1, pp. 179-192.
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Hassler, GW, Magee, AF, Zhang, Z, Baele, G, Lemey, P, Ji, X, Fourment, M & Suchard, MA 2023, 'Data Integration in Bayesian Phylogenetics', Annual Review of Statistics and Its Application, vol. 10, no. 1, pp. 353-377.
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Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the evolutionary history of a group of organisms, but also to understand the processes that guide its evolution and spread through space and time. To this end, it is now the norm to integrate numerous sources of data. For example, epidemiologists studying the spread of a virus through a region incorporate data including genetic sequences (e.g., DNA), time, location (both continuous and discrete), and environmental covariates (e.g., social connectivity between regions) into a coherent statistical model. Evolutionary biologists routinely do the same with genetic sequences, location, time, fossil and modern phenotypes, and ecological covariates. These complex, hierarchical models readily accommodate both discrete and continuous data and have enormous combined discrete/continuous parameter spaces including, at a minimum, phylogenetic tree topologies and branch lengths. The increasedsize and complexity of these statistical models have spurred advances in computational methods to make them tractable. We discuss both the modeling and computational advances, as well as unsolved problems and areas of active research.
Haydon, TD, Matthews, JL, Seymour, JR, Raina, J-B, Seymour, JE, Chartrand, K, Camp, EF & Suggett, DJ 2023, 'Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance', Proceedings of the Royal Society B: Biological Sciences, vol. 290, no. 1992.
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Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography–mass spectrometry (GC–MS)) to contrast metabolite profiles of
Pocillopora acuta
colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures,
P. acuta
predominantly associated with endosymbionts of the genera
Cladocopium
(reef) or
Durusdinium
(mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress,
P. acuta
endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove
P. acuta
populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.
Healey, AJ, Scholten, SC, Yang, T, Scott, JA, Abrahams, GJ, Robertson, IO, Hou, XF, Guo, YF, Rahman, S, Lu, Y, Kianinia, M, Aharonovich, I & Tetienne, J-P 2023, 'Quantum microscopy with van der Waals heterostructures', Nature Physics, vol. 19, no. 1, pp. 87-91.
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Hemsley, B, Darcy, S, Given, F, Murray, BR & Balandin, S 2023, 'Going thirsty for the turtles: Plastic straw bans, people with swallowing disability, and Sustainable Development Goal 14, Life Below Water', International Journal of Speech-Language Pathology, vol. 25, no. 1, pp. 15-19.
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Henry, JA, Szereday, S, Lynn, CK, Suggett, DJ, Camp, EF & Patterson, JT 2023, 'Using relative return‐on‐effort scoring to evaluate a novel coral nursery in Malaysia', Restoration Ecology, vol. 31, no. 3.
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Herdean, A, Hall, C, Hughes, DJ, Kuzhiumparambil, U, Diocaretz, BC & Ralph, PJ 2023, 'Temperature mapping of non-photochemical quenching in Chlorella vulgaris', Photosynthesis Research, vol. 155, no. 2, pp. 191-202.
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AbstractLight intensity and temperature independently impact all parts of the photosynthetic machinery in plants and algae. Yet to date, the vast majority of pulse amplitude modulated (PAM) chlorophyll a fluorescence measurements have been performed at well-defined light intensities, but rarely at well-defined temperatures. In this work, we show that PAM measurements performed at various temperatures produce vastly different results in the chlorophyte Chlorella vulgaris. Using a recently developed Phenoplate technique to map quantum yield of Photosystem II (Y(II)) and non-photochemical quenching (NPQ) as a function of temperature, we show that the fast-relaxing NPQ follows an inverse normal distribution with respect to temperature and appears insensitive to previous temperature acclimation. The slow-relaxing or residual NPQ after 5 minutes of dark recovery follows a normal distribution similar to Y(II) but with a peak in the higher temperature range. Surprisingly, higher slow- and fast-relaxing NPQ values were observed in high-light relative to low-light acclimated cultures. Y(II) values peaked at the adaptation temperature regardless of temperature or light acclimation. Our novel findings show the complete temperature working spectrum of Y(II) and how excess energy quenching is managed across a wide range of temperatures in the model microalgal species C. vulgaris. Finally, we draw attention to the fact that the effect of the temperature component in PAM measurements has been wildly underestimated, and results from experiments at room temperature can be misleading.
Hossain, KR, Turkewitz, DR, Holt, SA, Le Brun, AP & Valenzuela, SM 2023, 'Sterol Structural Features’ Impact on the Spontaneous Membrane Insertion of CLIC1 into Artificial Lipid Membranes', Langmuir, vol. 39, no. 9, pp. 3286-3300.
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Howlett, L, Camp, EF, Edmondson, J, Hosp, R, Taylor, B, Coulthard, P & Suggett, DJ 2023, 'Active coral propagation outcomes on coral communities at high-value Great Barrier Reef tourism sites', Biological Conservation, vol. 279, pp. 109930-109930.
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Johnston, NP, Piwczyński, M, Trzeciak, P, Walczak, K & Szpila, K 2023, 'Integration of mitogenomic and morphological data disentangles the systematics of Pollenia and establishes a revised phylogenetic hypothesis for the Polleniidae', Systematic Entomology, vol. 48, no. 2, pp. 296-315.
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Kannaujiya, VK, De Rubis, G, Paudel, KR, Manandhar, B, Chellappan, DK, Singh, SK, MacLoughlin, R, Gupta, G, Xenaki, D, Kumar, P, Hansbro, PM, Oliver, BGG, Wich, PR & Dua, K 2023, 'Anticancer activity of NFκB decoy oligonucleotide-loaded nanoparticles against human lung cancer', Journal of Drug Delivery Science and Technology, pp. 104328-104328.
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Kendig, MD, Hasebe, K, Tajaddini, A, Kaakoush, NO, Westbrook, RF & Morris, MJ 2023, 'The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive, and Gut Microbiome Parameters Are Preserved in Adult Rat Offspring of Mothers Fed a High‐Fat, High‐Sugar Diet', Molecular Nutrition & Food Research, vol. 67, no. 1, pp. 2200318-2200318.
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Kim, JH, Ajani, PA, Murray, SA, Kang, S-M, Kim, S-H, Lim, HC, Teng, ST, Lim, PT & Park, BS 2023, 'Abiotic and biotic factors controlling sexual reproduction in populations of Pseudo-nitzschia pungens (Bacillariophyceae)', Harmful Algae, vol. 123, pp. 102392-102392.
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Kofler, JR, Labeeuw, L, Bates, H, Zavafer, A & Ralph, PJ 2023, 'Light map optimization via direct chlorophyll fluorescence imaging in algal photobioreactors', Algal Research, vol. 71, pp. 103022-103022.
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L I, H, Huang, X, Cai, H, Herok, G, He, J, Su, Y, Li, W, Yi, C, Oliver, BG & Chen, H 2023, 'Mitochondrial dysfunction in a rat model and the related risk of metabolic disorders.', J Tradit Chin Med, vol. 43, no. 1, pp. 95-104.
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OBJECTIVE: To explore whether kidney deficiency (KYD) is prone to metabolic disorders may be linked to impaired mitochondrial function in thermogenesis and metabolic tissues. METHODS: A rat model of KYD was used, which was established using Sprague Dawley rat dams with warm preference subjected to herbal treatment that can improve kidney . The human relevance was confirmed by reduced serum corticosterone levels, and increased preference for warm location. RESULTS: KYD Rats were underdeveloped. Adenosine-triphosphate (ATP) production was reduced in the brown fat, but increased in the muscle. However, oxidative phosphorylated complexes to generate ATP and mitochondrial biogenesis marker were reduced in both tissues. When the second insult of high-fat diet (HFD) was introduced, KYD rats gained less weight yet developed more severe lipid and glucose metabolic disorders. This may be driven by disregulated liver gluconeogenesis marker forkhead box protein O1 and lipid metabolic regulator cholesterol 7 alpha-hydroxylase. CONCLUSION: KYD rats exhibited reduced mito-chondrial function in the brown fat, but were partially compensated by skeletal muscle, associated with the phenotype of warm preference and metabolic disorder, which was further exacerbated by additional HFD consumption. Future studies can focus on treatment targetting mitochondria function to reverse this phenotype.
Lam, MMC, Koong, J, Holt, KE, Hall, RM & Hamidian, M 2023, 'Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins', Microbiology Spectrum, vol. 11, no. 1.
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Though they contribute to the dissemination of genes that confer resistance to clinically important carbapenem and aminoglycoside antibiotics used to treat life-threatening
Acinetobacter baumannii
infections, plasmids found in
Acinetobacter
species have not been well studied. As these plasmids do not resemble those found in other Gram-negative pathogens, available typing systems are unsuitable.
Lane, M, Kashani, M, Barratt, JLN, Qvarnstrom, Y, Yabsley, MJ, Garrett, KB & Bradbury, RS 2023, 'Application of a universal parasite diagnostic test to biological specimens collected from animals', International Journal for Parasitology: Parasites and Wildlife, vol. 20, pp. 20-30.
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Lapine, M & Gorlach, M 2023, 'Current trends and nonlinear effects in multilayered metamaterials—FF-1:IL01', Ceramics International.
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Li, L, Cao, X, Huo, J, Qu, J, Chen, W, Liu, C, Zhao, Y, Liu, H & Wang, G 2023, 'High valence metals engineering strategies of Fe/Co/Ni-based catalysts for boosted OER electrocatalysis', Journal of Energy Chemistry, vol. 76, pp. 195-213.
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Li, Y, Faiz, A, Moshage, H, Schilling, L & Kamps, JAAM 2023, 'Responses of retinal and brain microvasculature to streptozotocin induced diabetes revealed by global expression profiling', Diabetes and Vascular Disease Research, vol. 20, no. 1, pp. 147916412211475-147916412211475.
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This study aims to determine the effects of diabetes in the retinal and brain microvasculature through gene expression profiling. Twelve male Wistar rats were randomly divided into two groups: streptozotocin-induced diabetic rats and time-matched nondiabetic rats. The retinal microvessels (RMVs) and brain microvessels (BMVs) were mechanically isolated from individual rats. Differentially expressed genes (DEGs) in diabetic and nondiabetic microvessels were identified by cDNA microarrays analysis. In RMVs, we identified 43 DEGs, of which 20 were upregulated while 23 were downregulated by diabetes. In BMVs, 35 genes DEGs were identified, of which 22 were upregulated and 13 were downregulated by diabetes. Altered expression of the Nars, Gars, Mars, Iars, Yars, Bcl2, Nqo1, NR4A3, Gpd1, Stc1, Tsc22d3, Tnfrsf21 mRNA as observed in the microarray analyses, was confirmed by quantitative RT-PCR. The aminoacyl-tRNA synthetases (aaRSs) pathway in RMVs was significantly overrepresented as compared to BMVs. Our study demonstrates for the first time that in the brain microvasculature multiple compensatory mechanisms exists, serving to protect brain tissue from diabetic insults, whereas these mechanisms are not activated in the retinal microvasculature. This provides new insights as to why brain microvasculature is less susceptible to diabetes.
Liu, L, Liu, Y, Zhang, X, Yuan, YL, Chen, ZH, Chen-Yu Hsu, A, Oliver, BG, Xie, M, Qin, L, Li, WM, Liu, D, Wang, G & Wood, LG 2023, 'Dyslipidemia Is Associated With Worse Asthma Clinical Outcomes: A Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 11, no. 3, pp. 863-872.e8.
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Machungo, CW, Berna, AZ, McNevin, D, Wang, R, Harvey, J & Trowell, S 2023, 'Evaluation of performance of metal oxide electronic nose for detection of aflatoxin in artificially and naturally contaminated maize', Sensors and Actuators B: Chemical, vol. 381, pp. 133446-133446.
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Matheson, S, Fleck, R, Irga, PJ & Torpy, FR 2023, 'Phytoremediation for the indoor environment: a state-of-the-art review', Reviews in Environmental Science and Bio/Technology, vol. 22, no. 1, pp. 249-280.
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AbstractPoor indoor air quality has become of particular concern within the built environment due to the time people spend indoors, and the associated health burden. Volatile organic compounds (VOCs) off-gassing from synthetic materials, nitrogen dioxide and harmful outdoor VOCs such benzene, toluene, ethyl-benzene and xylene penetrate into the indoor environment through ventilation and are the main contributors to poor indoor air quality with health effects. A considerable body of literature over the last four decades has demonstrate the removal of gaseous contaminants through phytoremediation, a technology that relies on plant material and technologies to remediate contaminated air streams. In this review we present a state-of-the-art on indoor phytoremediation over the last decade. Here we present a review of 38 research articles on both active and passive phytoremediation, and describe the specific chemical removal efficiency of different systems. The literature clearly indicates the efficacy of these systems for the removal of gaseous contaminants in the indoor environment, however it is evident that the application of phytoremediation technologies for research purposes in-situ is currently significantly under studied. In addition, it is common for research studies to assess the removal of single chemical species under controlled conditions, with little relevancy to real-world settings easily concluded. The authors therefore recommend that future phytoremediation research be conducted both in-situ and on chemical sources of a mixed nature, such as those experienced in the urban environment like petroleum vapour, vehicle emissions, and mixed synthetic furnishings off-gassing. The assessment of these systems both in static chambers for their theoretical performance, and in-situ for these mixed chemical sources is essential for the progression of th...
McNeilly, O, Mann, R, Cummins, ML, Djordjevic, SP, Hamidian, M & Gunawan, C 2023, 'Development of Nanoparticle Adaptation Phenomena in Acinetobacter baumannii: Physiological Change and Defense Response', Microbiology Spectrum, vol. 11, no. 1.
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Several recent studies have reported on the development of bacterial resistance to broad-spectrum antimicrobial silver nanoparticles (nanosilver; NAg). NAg is currently one of the most important alternative antimicrobial agents.
Menictas, M, Di Credico, G & Wand, MP 2023, 'Streamlined Variational Inference for Linear Mixed Models with Crossed Random Effects', Journal of Computational and Graphical Statistics, vol. 32, no. 1, pp. 99-115.
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Mohamad, MSB, Reyes, RJ, De Rubis, G, Paudel, KR, Hansbro, PM, Dua, K & Chellappan, DK 2023, 'THE VERSATILITY OF 18Β-GLYCYRRHETINIC ACID IN ATTENUATING PULMONARY INFLAMMATORY DISORDERS', EXCLI Journal, vol. 22, pp. 188-190.
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Moore, SJ, Deplazes, E & Mancera, RL 2023, 'Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide', Proteins: Structure, Function, and Bioinformatics, vol. 91, no. 3, pp. 338-353.
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Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein (IDP) whose abnormal aggregation into toxic soluble oligomers and insoluble amyloid fibrils is a pathological feature in type-2 diabetes. Rat IAPP (rIAPP) differs from hIAPP by only six amino acids yet has a reduced tendency to aggregate or form fibrils. The structures of the monomeric forms of IAPP are difficult to characterize due to their intrinsically disordered nature. Molecular dynamics simulations can provide a detailed characterization of the monomeric forms of rIAPP and hIAPP in near-physiological conditions. In this work, the conformational landscapes of rIAPP and hIAPP as a function of secondary structure content were predicted using well-tempered bias exchange metadynamics simulations. Several combinations of commonly used biomolecular force fields and water models were tested. The predicted conformational preferences of both rIAPP and hIAPP are typical of IDPs, exhibiting dominant random coil structures but showing a low propensity for transient α-helical conformations. Predicted nuclear magnetic resonance Cα chemical shifts reveal different preferences with each force field towards certain conformations, with AMBERff99SBnmr2/TIP4Pd showing the best agreement with the experiment. Comparisons of secondary structure content demonstrate residue-specific differences between hIAPP and rIAPP that may reflect their different aggregation propensities.
Morelato, M, Cadola, L, Bérubé, M, Ribaux, O & Baechler, S 2023, 'Forensic intelligence teaching and learning in higher education: An international approach', Forensic Science International, vol. 344, pp. 111575-111575.
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Muhammad, I, Ahmed, S, Cao, H, Mahmood, A & Wang, Y-G 2023, 'Three-Dimensional Silicene-Based Materials: A Universal Anode for Monovalent and Divalent Ion Batteries', The Journal of Physical Chemistry C, vol. 127, no. 2, pp. 1198-1208.
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Murrihy, RC, Drysdale, SAO, Dedousis-Wallace, A, Rémond, L, McAloon, J, Ellis, DM, Halldorsdottir, T, Greene, RW & Ollendick, TH 2023, 'Community-Delivered Collaborative and Proactive Solutions and Parent Management Training for Oppositional Youth: A Randomized Trial', Behavior Therapy, vol. 54, no. 2, pp. 400-417.
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Nguyen, LN, Vu, MT, Vu, HP, Johir, MAH, Labeeuw, L, Ralph, PJ, Mahlia, TMI, Pandey, A, Sirohi, R & Nghiem, LD 2023, 'Microalgae-based carbon capture and utilization: A critical review on current system developments and biomass utilization', Critical Reviews in Environmental Science and Technology, vol. 53, no. 2, pp. 216-238.
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Nickovic, S, Petković, S, Ilić, L, Pejanović, G, Mijić, Z, Huete, A & Marks, G 2023, 'Prediction of airborne pollen and sub-pollen particles for thunderstorm asthma outbreaks assessment', Science of The Total Environment, vol. 864, pp. 160879-160879.
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Noorian, P, Hoque, MM, Espinoza-Vergara, G & McDougald, D 2023, 'Environmental Reservoirs of Pathogenic Vibrio spp. and Their Role in Disease: The List Keeps Expanding', pp. 99-126.
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Patel, VK, Vishwas, S, Kumar, R, De Rubis, G, Shukla, SD, Paudel, KR, Manandhar, B, Singh, TG, Chellappan, DK, Gulati, M, Kaur, IP, Allam, VSRR, Hansbro, PM, Oliver, BG, MacLoughlin, R, Singh, SK & Dua, K 2023, 'Tackling the cytokine storm using advanced drug delivery in allergic airway disease', Journal of Drug Delivery Science and Technology, pp. 104366-104366.
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Pitiyarachchi, O, Lee, YC, Sim, H-W, Srirangan, S, Mapagu, C, Kirk, J, Harnett, PR, Balleine, RL, Bowtell, DDL, Samimi, G, Brand, AH, Marsh, DJ, Beale, P, Anderson, L, Bouantoun, N, Provan, P, Ramus, SJ, DeFazio, A & Friedlander, M 2023, 'Older age should not be a barrier to testing for somatic variants in homologous recombination DNA repair-related genes in patients with high-grade serous ovarian carcinoma', Translational Oncology, vol. 31, pp. 101638-101638.
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Power, T, Kennedy, P, Chen, H, Martinez-Maldonado, R, McGregor, C, Johnson, A, Townsend, L & Hayes, C 2023, 'Learning to Manage De-escalation Through Simulation: An Exploratory Study', Clinical Simulation in Nursing, vol. 77, pp. 23-29.
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Prasad, E, Atwood, L, van Oorschot, RAH, McNevin, D, Barash, M & Raymond, J 2023, 'Trace DNA recovery rates from firearms and ammunition as revealed by casework data', Australian Journal of Forensic Sciences, vol. 55, no. 1, pp. 73-88.
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Price, OF, Mikac, K, Wilson, N, Roberts, B, Critescu, RH, Gallagher, R, Mallee, J, Donatiou, P, Webb, J, Keith, DA, Letnic, M & Mackenzie, BDE 2023, 'Short‐term impacts of the 2019–20 fire season on biodiversity in eastern Australia', Austral Ecology, vol. 48, no. 1, pp. 3-11.
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Price, S, Kuzhiumparambil, U, Pernice, M, Herdean, A & Ralph, P 2023, 'Enhancement of cyanobacterial PHB production using random chemical mutagenesis with detection through FACS', Bioprocess and Biosystems Engineering, vol. 46, no. 2, pp. 297-306.
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Rahman, MK, Umashankar, B, Choucair, H, Pazderka, C, Bourget, K, Chen, Y, Dunstan, CR, Rawling, T & Murray, M 2023, 'Inclusion of the in-chain sulfur in 3-thiaCTU increases the efficiency of mitochondrial targeting and cell killing by anticancer aryl-urea fatty acids', European Journal of Pharmacology, vol. 939, pp. 175470-175470.
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Rathnayake, SNH, Ditz, B, van Nijnatten, J, Sadaf, T, Hansbro, PM, Brandsma, CA, Timens, W, van Schadewijk, A, Hiemstra, PS, ten Hacken, NHT, Oliver, B, Kerstjens, HAM, van den Berge, M & Faiz, A 2023, 'Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier', Respirology, vol. 28, no. 2, pp. 132-142.
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BACKGROUND AND OBJECTIVE: Smoking disturbs the bronchial-mucus-barrier. This study assesses the cellular composition and gene expression shifts of the bronchial-mucus-barrier with smoking to understand the mechanism of mucosal damage by cigarette smoke exposure. We explore whether single-cell-RNA-sequencing (scRNA-seq) based cellular deconvolution (CD) can predict cell-type composition in RNA-seq data. METHODS: RNA-seq data of bronchial biopsies from three cohorts were analysed using CD. The cohorts included 56 participants with chronic obstructive pulmonary disease [COPD] (38 smokers; 18 ex-smokers), 77 participants without COPD (40 never-smokers; 37 smokers) and 16 participants who stopped smoking for 1 year (11 COPD and 5 non-COPD-smokers). Differential gene expression was used to investigate gene expression shifts. The CD-derived goblet cell ratios were validated by correlating with staining-derived goblet cell ratios from the COPD cohort. Statistics were done in the R software (false discovery rate p-value < 0.05). RESULTS: Both CD methods indicate a shift in bronchial-mucus-barrier cell composition towards goblet cells in COPD and non-COPD-smokers compared to ex- and never-smokers. It shows that the effect was reversible within a year of smoking cessation. A reduction of ciliated and basal cells was observed with current smoking, which resolved following smoking cessation. The expression of mucin and sodium channel (ENaC) genes, but not chloride channel genes, were altered in COPD and current smokers compared to never smokers or ex-smokers. The goblet cell-derived staining scores correlate with CD-derived goblet cell ratios. CONCLUSION: Smoking alters bronchial-mucus-barrier cell composition, transcriptome and increases mucus production. This effect is partly reversible within a year of smoking cessation. CD methodology can predict goblet-cell percentages from RNA-seq.
Rathnayake, SNH, Ditz, B, Willemse, BWM, Timens, W, Kooistra, W, Heijink, IH, Oliver, BGG, van den Berge, M, Faiz, A, Aliee, H, Theis, FJ & Nawijn, MC 2023, 'Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome', Chest.
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Reich, HG, Camp, EF, Roger, LM & Putnam, HM 2023, 'The trace metal economy of the coral holobiont: supplies, demands and exchanges', Biological Reviews, vol. 98, no. 2, pp. 623-642.
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Rourke, ML, Walburn, JW, Broadhurst, MK, Fowler, AM, Hughes, JM, Fielder, DS, DiBattista, JD & Furlan, EM 2023, 'Poor utility of environmental DNA for estimating the biomass of a threatened freshwater teleost; but clear direction for future candidate assessments', Fisheries Research, vol. 258, pp. 106545-106545.
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Russell, K, Kelty, SF & Scudder, N 2023, 'Public and family support and concerns for providing DNA to law enforcement in long-term missing person cases', Science & Justice, vol. 63, no. 2, pp. 149-157.
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Safaei, J, Gao, Y, Hosseinpour, M, Zhang, X, Sun, Y, Tang, X, Zhang, Z, Wang, S, Guo, X, Wang, Y, Chen, Z, Zhou, D, Kang, F, Jiang, L & Wang, G 2023, 'Vacancy Engineering for High-Efficiency Nanofluidic Osmotic Energy Generation', Journal of the American Chemical Society, vol. 145, no. 4, pp. 2669-2678.
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Scanes, E & Byrne, M 2023, 'Warming and hypoxia threaten a valuable scallop fishery: A warning for commercial bivalve ventures in climate change hotspots', Global Change Biology, vol. 29, no. 8, pp. 2043-2045.
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Scanes, E, Ross, PM, Seymour, JR, Siboni, N, Dove, MC, O'Connor, WA, Dittes, C & Parker, LM 2023, 'Transgenerational transfer of the microbiome is altered by ocean acidification in oyster larvae', Aquaculture, vol. 565, pp. 739153-739153.
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Scaramuzzo, G, Nucera, F, Asmundo, A, Messina, R, Mari, M, Montanaro, F, Johansen, MD, Monaco, F, Fadda, G, Tuccari, G, Hansbro, NG, Hansbro, PM, Hansel, TT, Adcock, IM, David, A, Kirkham, P, Caramori, G, Volta, CA & Spadaro, S 2023, 'Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance.', J Inflamm (Lond), vol. 20, no. 1, p. 11.
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The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.
Szpila, K, Piwczyński, M, Glinkowski, W, Lutz, L, Akbarzadeh, K, Baz, A, Johnston, NP & Grzywacz, A 2023, 'First molecular phylogeny and species delimitation of West Palaearctic Pollenia (Diptera: Polleniidae)', Zoological Journal of the Linnean Society, vol. 197, no. 1, pp. 267-282.
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Abstract
Cluster flies of the genus Pollenia are known as mass invaders of human dwellings, but are important plant pollinators in the temperate climatic zone. Despite being the most species-rich and widespread genus in Polleniidae, no study to date has tested infrageneric relationships using molecular data. Here we use three molecular markers, COI, Ef-1α and CAD to reconstruct the phylogenetic relationships between 18 West Palaearctic species of Pollenia, representing eight predefined morphological species groups, using both maximum likelihood and Bayesian approaches. We show several instances where morphological and molecular results are congruent, but also instances where they are discordant. We develop a COI barcode reference library for 18 species, containing newly generated data (87 sequences) and sequences retrieved from the Barcode of Life Data System (BOLD). We analyse this dataset using both Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics & Phylogeography (BPP) methods to validate morphological species hypotheses and delimit species. The results of these species delimitation analyses were, in most cases, identical and aligned with predefined morphological species concepts. Based on the results of our analyses, we synonymize P. moravica (stat. rev.) with P. amentaria and assign 191 unidentified sequences from BOLD to named morphospecies.
Tang, Y, Ma, S, Lin, S, Wu, Y, Chen, S, Liu, G, Ma, L, Wang, Z, Jiang, L & Wang, Y 2023, 'Cell-free protein synthesis of CD1E and B2M protein and in vitro interaction', Protein Expression and Purification, vol. 203, pp. 106209-106209.
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Tu, L, Wu, K, Luo, Y, Wang, E, Yuan, J, Zuo, J, Zhou, D, Li, B, Zhou, J, Jin, D & Zhang, H 2023, 'Significant Enhancement of the Upconversion Emission in Highly Er 3+ ‐Doped Nanoparticles at Cryogenic Temperatures', Angewandte Chemie International Edition, vol. 62, no. 7.
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Tu, L, Wu, K, Luo, Y, Wang, E, Yuan, J, Zuo, J, Zhou, D, Li, B, Zhou, J, Jin, D & Zhang, H 2023, 'Significant Enhancement of the Upconversion Emission in Highly Er 3+ ‐Doped Nanoparticles at Cryogenic Temperatures', Angewandte Chemie, vol. 135, no. 7.
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van Oppen, MJH & Raina, J 2023, 'Coral holobiont research needs spatial analyses at the microbial scale', Environmental Microbiology, vol. 25, no. 1, pp. 179-183.
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Verma, A, Hoppenrath, M, Smith, KF, Murray, JS, Harwood, DT, Hosking, JM, Rongo, T, Rhodes, LL & Murray, SA 2023, 'Ostreopsis Schmidt and Coolia Meunier (Dinophyceae, Gonyaulacales) from Cook Islands and Niue (South Pacific Ocean), including description of Ostreopsis tairoto sp. nov.', Scientific Reports, vol. 13, no. 1, pp. 3110-3110.
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AbstractIt is important to decipher the diversity and distribution of benthic dinoflagellates, as there are many morphologically indistinct taxa that differ from one another in production of potent toxins. To date, the genus Ostreopsis comprises twelve described species, of which seven are potentially toxic and produce compounds presenting a threat to human and environmental health. In this study, isolates previously identified as “Ostreopsis sp. 3” were sampled from the area where it was first reported, Rarotonga, Cook Islands, and have been taxonomically and phylogenetically characterised as Ostreopsis tairoto sp. nov. Phylogenetically, the species is closely related to “Ostreopsis sp. 8”, O. mascarenensis, “O. sp. 4”, O. fattorussoi, O. rhodesiae and O. cf. siamensis. Previously, it was considered a part of the O. cf. ovata complex but can be distinguished from O. cf. ovata based on the small pores identified on this study, and from O. fattorussoi and O. rhodesiae based on relative lengths of the 2′ plates. No known palytoxin -like compounds were detected in strains investigated in this study. Strains of O. lenticularis, Coolia malayensis and C. tropicalis were also identified and described. This study advances our knowledge of biogeography, distribution, and toxins of Ostreopsis and Coolia species.
Wang, J, Zhang, X, Zhang, L, Liu, Y, Wang, G, Zhang, HP, Wang, L, Kang, DY, Oliver, BG, Wan, HJ, McDonald, VM, Chen-Yu Hsu, A, Liu, D, Li, WM, Birring, SS & Wang, G 2023, 'Age-Related Clinical Characteristics, Inflammatory Features, Phenotypes, and Treatment Response in Asthma', The Journal of Allergy and Clinical Immunology: In Practice, vol. 11, no. 1, pp. 210-219.e3.
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Wang, Y, Wang, X, Jia, X, Li, J, Fu, J, Huang, X, Cui, X, Wang, B, Luo, W, Lin, C, Li, Z, Luu, LDW, Li, S, Zhu, X & Tai, J 2023, 'Influenza vaccination features revealed by a single‐cell transcriptome atlas', Journal of Medical Virology, vol. 95, no. 1.
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Webb, JK, Jolly, CJ, Hinds, M, Adams, C, Cuartas‐Villa, S, Lapwong, Y & Letnic, M 2023, 'Effects of the Australian 2019–2020 megafires on a population of endangered broad‐headed snakes Hoplocephalus bungaroides', Austral Ecology, vol. 48, no. 1, pp. 24-30.
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Webster, J, Dadd‐Daigle, P, Chapman, TA & Kirkby, K 2023, 'Investigating the defoliating‐like (DL) VCG2A pathotype of Verticillium dahliae through identification and prediction of secreted proteins from genomes of Australian isolates', Plant Pathology, vol. 72, no. 2, pp. 334-341.
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Wei, X, Li, R, Li, X, Wang, B, Huang, J, Mu, H, Zhang, Q, Zhang, Z, Ru, Y, Wu, X, Qiu, Y, Ye, Y, Feng, Y, Wang, S, Chen, H, Yi, C & Wang, J 2023, 'iPSCs-derived mesenchymal stromal cells mitigate anxiety and neuroinflammation in aging female mice', The International Journal of Biochemistry & Cell Biology, vol. 155, pp. 106347-106347.
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Wong, LL, Mugunthan, S, Kundukad, B, Ho, JCS, Rice, SA, Hinks, J, Seviour, T, Parikh, AN & Kjelleberg, S 2023, 'Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix', Environmental Microbiology, vol. 25, no. 1, pp. 199-208.
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Woodward, H, Moret, S & Chadwick, S 2023, 'Biodegradable plastics and their impact on fingermark detection methods', Forensic Science International, vol. 344, pp. 111571-111571.
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Wu, B, Chen, C, Raijmakers, LHJ, Liu, J, Danilov, DL, Eichel, R-A & Notten, PHL 2023, 'Li-growth and SEI engineering for anode-free Li-metal rechargeable batteries: A review of current advances', Energy Storage Materials, vol. 57, pp. 508-539.
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Xie, Q, Moore, CE, Cleverly, J, Hall, CC, Ding, Y, Ma, X, Leigh, A & Huete, A 2023, 'Land surface phenology indicators retrieved across diverse ecosystems using a modified threshold algorithm', Ecological Indicators, vol. 147, pp. 110000-110000.
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Yamaguchi, A, Hoppenrath, M, Murray, S, Kretzschmar, AL, Horiguchi, T & Wakeman, KC 2023, 'Morphology and molecular phylogeny of the benthic dinoflagellates (Dinophyceae, Peridiniales) Amphidiniopsis crumena n. sp. and Amphidiniopsis nileribanjensis n. sp.', European Journal of Protistology, vol. 87, pp. 125940-125940.
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Zhand, S, Zhu, Y, Nazari, H, Sadraeian, M, Warkiani, ME & Jin, D 2023, 'Thiolate DNAzymes on Gold Nanoparticles for Isothermal Amplification and Detection of Mesothelioma-derived Exosomal PD-L1 mRNA', Analytical Chemistry, vol. 95, no. 6, pp. 3228-3237.
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Zhigulin, I, Yamamura, K, Ivády, V, Gale, A, Horder, J, Lobo, CJ, Kianinia, M, Toth, M & Aharonovich, I 2023, 'Photophysics of blue quantum emitters in hexagonal boron nitride', Materials for Quantum Technology, vol. 3, no. 1, pp. 015002-015002.
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Abstract
Colour centres in hexagonal boron nitride (hBN) have emerged as intriguing contenders for integrated quantum photonics. In this work, we present a detailed photophysical analysis of hBN single emitters emitting at the blue spectral range. The emitters are fabricated by different electron beam irradiation and annealing conditions and exhibit narrow-band luminescence centred at 436 nm. Photon statistics as well as rigorous photodynamics analysis unveils potential level structure of the emitters, which suggests lack of a metastable state, supported by a theoretical analysis. The potential defect can have an electronic structure with fully occupied defect state in the lower half of the hBN band gap and empty defect state in the upper half of the band gap. Overall, our results are important to understand the photophysical properties of the emerging family of blue quantum emitters in hBN as potential sources for scalable quantum photonic applications.
Zong, L, Yu, Y, Wang, J, Liu, P, Feng, W, Dai, X, Chen, L, Gunawan, C, Jimmy Yun, SL, Amal, R, Cheong, S, Gu, Z & Chen, Y 2023, 'Oxygen-vacancy-rich molybdenum carbide MXene nanonetworks for ultrasound-triggered and capturing-enhanced sonocatalytic bacteria eradication', Biomaterials, vol. 296, pp. 122074-122074.
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